**From:** Eric H. Lee (*ericlee_at_ks.uiuc.edu*)

**Date:** Mon May 11 2009 - 23:49:25 CDT

**Next message:**Roman Petrenko: "namd-cuda-intel vs. namd-intel"**Previous message:**Joshua Adelman: "Re: Calculating displacement in a system with periodic boundary"**In reply to:**Fred (Rui FENG): "Calculating displacement in a system with periodic boundary"**Next in thread:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Reply:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

You can choose not to wrap the system coordinates during the

simulation, but keeping the periodic boundary conditions in place.

The options in the namd script are "wrapall" and "wrapwater" I believe.

You might also try unwrapping your existing trajectory using PBCtools:

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

-Eric

On May 11, 2009, at 11:26 PM, Fred (Rui FENG) wrote:

*> Hi All,
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*>
*

*> I have a question that can be simplified like this:
*

*>
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*> Suppose there's a cube with lots of particles/atoms. The boundary is
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*> periodic and only Lennard Jones force field is in the system. All
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*> atoms are moving with random velocities. The velocity of the center
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*> of mass could not be zero. I have a common DCD file with coordinates
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*> of all atoms. My question is: how to get the displacement of all
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*> atoms?
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*>
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*> I cannot just simply subtract the coordinate of one atom from the
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*> coordinate of the same atom in the previous frame. Supposing the
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*> cube has 200 edge length and the center is (0,0,0). If a atom at the
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*> position (99, 0, 0) moves to the position (-99, 0, 0), the
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*> displacement could be either 2 or -198 because of the periodic
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*> boundary. The absolute coordinate could be (102, 0, 0), but in the
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*> DCD file it's (-99, 0, 0). It makes the displacement calculation
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*> impossible.
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*>
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*> So I was wondering if there are any ways with which NAMD can output
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*> a "modified" DCD file with absolute coordinates. Thank you!
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*>
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*> Have a nice day!
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*>
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*> Fred
*

Eric H. Lee

Medical Scholars Program

Theoretical and Computational Biophysics Group, UIUC

ericlee_at_ks.uiuc.edu

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